topFuncs: Functions from Bases to Topological Properties

Description

A collection of functions which return topological properties given a base. These functions are intented to be used with those in the Fast Model Analysis section. Note that these functions have very different inputs.

Usage

fWidths(nodeDists)
fAvgLadder(ladderNumbers)
fNLadders(ladderNumbers)
fColless(treeImbalance)
fNConfig(nTipDes,configSize)

Arguments

nodeDists

The result of running dists on a tree. That is, a vector organised by nodeId giving the distance of each node from the root.

ladderNumbers

The result of running ladderNums on a tree. That is, a vector organised by nodeId giving the largest ladder size going away from the root starting from each node.

treeImbalance

The result of running treeImb on a tree. See treeImb for more information.

nTipDes

The result of running nTipDescendants on a tree. That is, a vector organised by nodeId giving the number of tip descendants of each node.

configSize

An integer specifying the size of configuration to count.

Value

These functions all have the same value as their corresponding function.

Details

These functions all correspond to other functions based on trees. For example, fColless corresponds to colless. These functions are much faster but take inputs which already require a reasonable amount of work to calculate. To learn more about fColless see the documentation for colless. For example, the intention is that when calculating many topological properties it may be faster to calculate ladderNumbers and nodeDists first and then run these functions.

Examples

Run this code

## Sets up an example tree
tree <- rtree4(50)

## This returns the same ouput as avgLadder(tree)
ladderNumbers <- ladderNums(tree)
fAvgLadder(ladderNumbers)

## But now we can calculate the number of ladders more efficiently.
fNLadders

Run the code above in your browser using DataLab

Last chance! 50% off unlimited learning